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Example Resistance Gene Identifier (RGI) v6.0.6 Genotype Data from EuSCAPE project

Source: R/data.R
rgi_EuSCAPE_raw.Rd

Raw RGI v6.0.6 results file for Klebsiella pneumoniae from EuSCAPE project, one AMR determinant per row. Includes only Perfect and Strict hits Samples IDs that have no AMR markers were added to the ORF_ID column with remaining blank rows since RGI will generate blank outputs for these samples Columns Predicted_DNA, Predicted_Protein, and CARD_Protein_Sequence were removed to reduce file size.

Usage

rgi_EuSCAPE_raw

Format

rgi_EuSCAPE_raw A data frame with 59,448 rows and 25 columns:

  • ORF_ID: Sample identifier

  • ...: RGI results columns

Source

ENA BioProject PRJEB10018. See David et al. (2019) https://doi.org/10.1038/s41564-019-0492-8.